pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
		 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
		 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<parent>
		<groupId>org.springframework.boot</groupId>
		<artifactId>spring-boot-starter-parent</artifactId>
		<version>3.1.5</version>
		<relativePath/> <!-- lookup parent from repository -->
	</parent>
	<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
	<artifactId>pic-sure-hpds</artifactId>
	<version>3.0.0-SNAPSHOT</version>
	<packaging>pom</packaging>
	<name>pic-sure-hpds</name>
	<modules>
		<module>common</module>
		<module>service</module>
		<module>etl</module>
		<module>data</module>
		<module>processing</module>
		<module>client-api</module>
		<module>genomic-processor</module>
		<module>docker</module>
		<module>war</module>
    </modules>
	<properties>
		<maven.compiler.release>21</maven.compiler.release>
		<java.version>21</java.version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<dockerfile-maven-version>1.4.10</dockerfile-maven-version>
		<aws.version>2.20.153</aws.version>
		<spotless.version>2.41.1</spotless.version>
	</properties>
	<repositories>
		<repository>
			<id>github</id>
			<name>GitHub HMS-DBMI Apache Maven Packages</name>
			<url>https://maven.pkg.github.com/hms-dbmi/pic-sure</url>
			<snapshots>
				<enabled>true</enabled>
			</snapshots>
		</repository>
	</repositories>
	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-dependency-plugin</artifactId>
					<version>2.8</version>
					<executions>
						<execution>
							<id>copy-installed</id>
							<phase>install</phase>
							<goals>
								<goal>copy</goal>
							</goals>
							<configuration>
								<artifactItems>
									<artifactItem>
										<groupId>${project.groupId}</groupId>
										<artifactId>${project.artifactId}</artifactId>
										<version>${project.version}</version>
										<type>${project.packaging}</type>
									</artifactItem>
								</artifactItems>
								<outputDirectory>pic-sure-hpds</outputDirectory>
							</configuration>
						</execution>
					</executions>
				</plugin>

				<plugin>
					<groupId>org.apache.tomcat.maven</groupId>
					<artifactId>tomcat7-maven-plugin</artifactId>
					<version>2.0</version>
					<executions>
						<execution>
							<id>default-cli</id>
							<goals>
								<goal>run</goal>
							</goals>
							<configuration>
								<port>13000</port>
								<path>/jaxrs-service</path>
								<useSeparateTomcatClassLoader>true</useSeparateTomcatClassLoader>
								<jpda>true</jpda>
								<systemProperties>
									<JAVA_OPTS>-Xms256m -Xmx512m</JAVA_OPTS>
								</systemProperties>
							</configuration>
						</execution>
					</executions>
					<configuration>
					</configuration>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-eclipse-plugin</artifactId>
					<configuration>
						<projectNameTemplate>[artifactId]-[version]</projectNameTemplate>
						<wtpmanifest>true</wtpmanifest>
						<wtpapplicationxml>true</wtpapplicationxml>
						<wtpversion>2.0</wtpversion>
					</configuration>
				</plugin>
				<plugin>
					<groupId>com.diffplug.spotless</groupId>
					<artifactId>spotless-maven-plugin</artifactId>
					<version>${spotless.version}</version>
					<configuration>
						<java>
							<eclipse>
								<version>4.26</version>
								<file>code-formatting/eclipse-formatter.xml</file>
							</eclipse>
							<toggleOffOn />
						</java>
					</configuration>
				</plugin>

				<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
				<plugin>
					<artifactId>maven-clean-plugin</artifactId>
					<version>3.1.0</version>
				</plugin>
				<!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
				<plugin>
					<artifactId>maven-resources-plugin</artifactId>
					<version>3.0.2</version>
				</plugin>
				<plugin>
					<artifactId>maven-compiler-plugin</artifactId>
					<version>3.8.0</version>
					<configuration>
						<!--this is the target Java version-->
						<release>21</release>
					</configuration>
				</plugin>
				<plugin>
					<artifactId>maven-surefire-plugin</artifactId>
					<version>2.22.1</version>
				</plugin>
				<plugin>
					<artifactId>maven-jar-plugin</artifactId>
					<version>3.0.2</version>
				</plugin>
				<plugin>
					<artifactId>maven-install-plugin</artifactId>
					<version>2.5.2</version>
				</plugin>
				<plugin>
					<artifactId>maven-deploy-plugin</artifactId>
					<version>2.8.2</version>
				</plugin>
				<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
				<plugin>
					<artifactId>maven-site-plugin</artifactId>
					<version>3.7.1</version>
				</plugin>
				<plugin>
					<artifactId>maven-project-info-reports-plugin</artifactId>
					<version>3.0.0</version>
				</plugin>
			</plugins>
		</pluginManagement>
	</build>
	<dependencies>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-test</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.springframework.boot</groupId>
			<artifactId>spring-boot-starter-web</artifactId>
		</dependency>
	</dependencies>
	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>org.springframework.boot</groupId>
				<artifactId>spring-boot-starter-tomcat</artifactId>
				<scope>provided</scope>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>common</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>client-api</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>service</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>processing</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>etl</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach.hpds</groupId>
				<artifactId>data</artifactId>
				<version>${project.version}</version>
			</dependency>
			<dependency>
				<groupId>edu.harvard.hms.dbmi.avillach</groupId>
				<artifactId>pic-sure-resource-api</artifactId>
				<version>2.2.0-SNAPSHOT</version>
				<exclusions>
					<exclusion>
						<groupId>org.apache.logging.log4j</groupId>
						<artifactId>log4j-core</artifactId>
					</exclusion>
					<exclusion>
						<groupId>org.slf4j</groupId>
						<artifactId>slf4j-log4j12</artifactId>
					</exclusion>
					<exclusion>
						<groupId>org.slf4j</groupId>
						<artifactId>slf4j-api</artifactId>
					</exclusion>
					<exclusion>
						<groupId>ch.qos.logback</groupId>
						<artifactId>logback-classic</artifactId>
					</exclusion>
					<exclusion>
						<groupId>org.slf4j</groupId>
						<artifactId>slf4j-jdk14</artifactId>
					</exclusion>
				</exclusions>
			</dependency>
			<dependency>
				<groupId>com.google.guava</groupId>
				<artifactId>guava</artifactId>
				<version>32.0.0-jre</version>
			</dependency>
			<dependency>
				<groupId>org.apache.commons</groupId>
				<artifactId>commons-math3</artifactId>
				<version>3.6.1</version>
			</dependency>
			<dependency>
				<groupId>de.siegmar</groupId>
				<artifactId>fastcsv</artifactId>
				<version>1.0.2</version>
			</dependency>
			<dependency>
				<groupId>org.apache.commons</groupId>
				<artifactId>commons-csv</artifactId>
				<version>1.5</version>
			</dependency>
			<dependency>
				<groupId>commons-io</groupId>
				<artifactId>commons-io</artifactId>
				<version>2.14.0</version>
			</dependency>
			<dependency>
				<groupId>org.codehaus.jackson</groupId>
				<artifactId>jackson-core-asl</artifactId>
				<version>${jackson.version}</version>
			</dependency>
			<dependency>
				<groupId>org.codehaus.jackson</groupId>
				<artifactId>jackson-mapper-asl</artifactId>
				<version>${jackson.version}</version>
			</dependency>
			<dependency>
				<groupId>javax.xml.bind</groupId>
				<artifactId>jaxb-api</artifactId>
				<version>2.3.0</version>
			</dependency>
			<dependency>
				<groupId>com.sun.xml.bind</groupId>
				<artifactId>jaxb-core</artifactId>
				<version>2.3.0</version>
			</dependency>
			<dependency>
				<groupId>com.sun.xml.bind</groupId>
				<artifactId>jaxb-impl</artifactId>
				<version>2.3.0</version>
			</dependency>
			<dependency>
				<groupId>javax.activation</groupId>
				<artifactId>activation</artifactId>
				<version>1.1.1</version>
			</dependency>
			<dependency>
				<groupId>org.mockito</groupId>
				<artifactId>mockito-core</artifactId>
				<version>3.8.0</version>
				<scope>test</scope>
			</dependency>
			<dependency>
				<groupId>com.oracle.database.jdbc</groupId>
				<artifactId>ojdbc10</artifactId>
				<version>19.17.0.0</version>
			</dependency>
			<dependency>
				<groupId>com.github.ben-manes.caffeine</groupId>
				<artifactId>caffeine</artifactId>
				<version>3.1.1</version>
			</dependency>
			<dependency>
				<groupId>io.projectreactor.netty</groupId>
				<artifactId>reactor-netty</artifactId>
				<version>1.1.12</version>
			</dependency>
			<dependency>
				<groupId>com.fasterxml.jackson.core</groupId>
				<artifactId>jackson-databind</artifactId>
				<version>2.15.3</version>
			</dependency>
			<dependency>
				<groupId>org.projectlombok</groupId>
				<artifactId>lombok</artifactId>
				<version>1.18.30</version>
				<scope>provided</scope>
			</dependency>
			<dependency>
				<groupId>org.apache.avro</groupId>
				<artifactId>avro</artifactId>
				<version>1.12.0</version>
			</dependency>
			<dependency>
				<groupId>org.xerial.snappy</groupId>
				<artifactId>snappy-java</artifactId>
				<version>1.1.10.5</version>
			</dependency>
			<dependency>
				<groupId>software.amazon.awssdk</groupId>
				<artifactId>s3</artifactId>
				<version>${aws.version}</version>
				<exclusions>
					<!--Spring boot will complain about this dep on startup. It's not needed (we use SLF4J + Logback)-->
					<exclusion>
						<groupId>commons-logging</groupId>
						<artifactId>commons-logging</artifactId>
					</exclusion>
				</exclusions>
			</dependency>

    </dependencies>
  </dependencyManagement>
  <distributionManagement>
    <repository>
      <id>github</id>
      <name>GitHub HMS-DBMI Apache Maven Packages</name>
      <url>https://maven.pkg.github.com/hms-dbmi/pic-sure-hpds</url>
    </repository>
  </distributionManagement>
</project>